Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: NTFQ01003429.1 Kokia drynarioides strain JFW-HI SEQ_116201, whole genome shotgun sequence Parameters: 2 7 7 80 10 50 1000 Pmatch=0.80,Pindel=0.10 tuple sizes 0,4,5,7 tuple distances 0, 29, 159, 834 Length: 1390 ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29 Found at i:411 original size:214 final size:213 Alignment explanation
Indices: 12--1390 Score: 1155 Period size: 214 Copynumber: 6.5 Consensus size: 213 2 TTCAAAAAAT * * * * * 12 AAAAGCTGTTTACAAAATGACAACTATTT-GA-CATAATGTTGTGATTTTCCAGGCATGGACTGT 1 AAAAGTTGTTTACAAAATGACAACTATTTAGACCA-AATGATGCGA--TTCCAAGCATGGAATGT * * * * * 75 ACAGAAAATTACTCGAAGGAATCGATCGTCTTGAATACGTTAATGAACAAAAGTTATAAAAGAAC 63 TCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAAC * * * * * * * * * 140 TCGTAAATGTTTGTCAAGTTTA-AAGTTCGGTCGAG-AACTAAGAAAGAAACAATTCTCACATAA 128 ACGTAAAAGTTTGTCAACTTCAGAAGTTTGGCCGAGAAAC-AAGAGAGAAACTATTCTCACCTAA * 203 ATAATTTTTTAATTCAAAGACC 192 ATAAGTTTTTAATTCAAAGACC * * * * ** * 225 AAAAGTTGTTTACAAAACGATAACTAGTTAGACCAAATGATGAGATTCCCTGTGCTTGGAATGTT 1 AAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGATT-CC-AAGCATGGAATGTT * * * * ** 290 CAGAAAATTGCTCGAAGGAATGGTTTGTCTTGATTACTGTAAGGAACTGAAGTTAT-AAAGAACA 64 CAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACA * * 354 CGTAAAAGTTTGTCAACTTCAGAAGTTTGGCCTAGAAACAAGAGAGAAACTATTCTCACCTAAAA 129 CGTAAAAGTTTGTCAACTTCAGAAGTTTGGCCGAGAAACAAGAGAGAAACTATTCTCACCTAAAT * * 419 AAGTTTATAATTCAGAGACC 194 AAGTTTTTAATTCAAAGACC * * * * * * * 439 AAAAGTTGTTTACATAATGGCAATTATTTACACTAAATGATGCGATTTCTAGAGCATAGAAT-TT 1 AAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGA-TTCCA-AGCATGGAATGTT ** 503 CTTAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCAAAA-TTAT-AAAGTAA 64 CAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-CAAAAGTTATAAAAG-AA * * * * ** * * * * 566 CTCGTAAAAGTTTTTCAAGC-TCGGAAGTTAGATCGAGAACCAAAAGAGAAACAATTCTCAACTA 127 CACGTAAAAGTTTGTCAA-CTTCAGAAGTTTGGCCGAGAAACAAGAGAGAAACTATTCTCACCTA * * * 630 AATAAATTTTTCATT-AGAAGACT 191 AATAAGTTTTTAATTCA-AAGACC * * * * * * * 653 AGAAGTAGTTTAAAAAATGACAACT-TTTAGACCTAATGATGTGATTTTCCAAGCATGGACTGTA 1 AAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGA--TTCCAAGCATGGAATGTT * * * * * * * 717 CAGAAAATTACTCGAAGGAATCGATCTTCTTGAATACTTTAATGAGCAAAAGTTATAAAAGTACT 64 CAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACA * * * * 782 CGTAAAACTTTG------TC--AAGTTCGGCTGAG-AACGAATAGAGAAA-TAATTCTCACCTAA 129 CGTAAAAGTTTGTCAACTTCAGAAGTTTGGCCGAGAAAC-AAGAGAGAAACT-ATTCTCACCTAA * * 837 ATAAGTTTTTAATTGAAAAACC 192 ATAAGTTTTTAATTCAAAGACC * * * * * * * * * * 859 GAAAGTAG-TTATAGAATGAC-AGTAATTTAGACCTAATAATGTGATTTCCCAAGCACGGACTGT 1 AAAAGTTGTTTACAAAATGACAACT-ATTTAGACCAAATGATGCGA-TT-CCAAGCATGGAATGT * * * * * 922 ACA-ATATATTG-TTGAAGGAATGGATCGTCTTGAATACTTTAATGAACAAAATTTATAAAAGAA 63 TCAGA-AAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAA * * * * * * * * 985 CATG-AAAATTTTGTCAAGTTTA-AAGTTTGGCCGAGAACCAAGAAAGAAAC-AGCTATCACCTA 127 CACGTAAAAGTTTGTCAACTTCAGAAGTTTGGCCGAGAAACAAGAGAGAAACTA-TTCTCACCTA * * 1047 AAGAATTTTTTAATTCAAAGACC 191 AATAAGTTTTTAATTCAAAGACC * * * * 1070 AAAAGTTGTTTACAAAAAGACAACTATTTAAACAAAATGATGCGATTTCCAAGCATGGAAAGTTC 1 AAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGA-TTCCAAGCATGGAATGTTC * * * * 1135 AAAAAATTGCTCGAAGGAATGGATCGTCTTAAATACTTTAAGGAGCCAAAGTTATAAAAGAA-AT 65 AGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACA- * * * * * * 1199 CGTAAAAGTTTGTCAACTT-TGAAAGTTCGGCCCAGAACCAAGAGAGAAATTATTCTTACCTAAA 129 CGTAAAAGTTTGTCAACTTCAG-AAGTTTGGCCGAGAAACAAGAGAGAAACTATTCTCACCTAAA * 1263 TAAGTTTTTAATTCAAAGATC 193 TAAGTTTTTAATTCAAAGACC * * * * * 1284 AAAAGTTGTTTACATAATAACATCTATTTAGACCAAATGGTGCGATTTCTCGAGCATGGAATGTT 1 AAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGA-TTC-CAAGCATGGAATGTT * * * 1349 CCAG-AAATTGCTCGAAGGAATAGATCGTCTTGATTGCTTTAA 64 -CAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAA Statistics Matches: 932, Mismatches: 190, Indels: 86 0.77 0.16 0.07 Matches are distributed among these distances: 204 10 0.01 205 64 0.07 206 90 0.10 207 1 0.00 208 2 0.00 210 2 0.00 211 72 0.08 212 79 0.08 213 147 0.16 214 403 0.43 215 60 0.06 216 2 0.00 ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29 Consensus pattern (213 bp): AAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGATTCCAAGCATGGAATGTTCA GAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACACG TAAAAGTTTGTCAACTTCAGAAGTTTGGCCGAGAAACAAGAGAGAAACTATTCTCACCTAAATAA GTTTTTAATTCAAAGACC Found at i:1126 original size:417 final size:420 Alignment explanation
Indices: 79--1390 Score: 1203 Period size: 427 Copynumber: 3.1 Consensus size: 420 69 GACTGTACAG * * * * 79 AAAATTACTCGAAGGAATCGATCGTCTTGAATACGTTAATGAACAAAAGTTATAAAAGAACTCGT 1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAATGAACAAAA-TTATAAAAGAACTCGA * * * 144 AAATGTTTGTCAAGTTTAAAGTTCGGTCGAGAACTAAGAAAGAAACAATTCTCACATAAATAATT 65 AAAT-TTTGTCAAGTTTAAAGTTAGGTCGAGAACCAAGAAAGAAACAATTCTCACCTAAATAATT * * * * 209 TTTTAATTCAAAGACCAAAAGTTGTTTACAAAACGATAACTAGTTAGACCAAATGATGAGATTCC 129 TTTTAATTCAAAGACCAAAAGTTGTTTACAAAAAGACAACTATTTAGACCAAATGATGAGATTTC ** * * * * * * ** 274 CTGTGCTTGGAATGTTCAGAAAATTGCTCGAAGGAATGGTTTGTCTTGATTACTGTAAGGAACTG 194 C-AAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGATCT-TCTTGAATACTTTAAGGAGCAA * * 339 AAGTTAT-AAAGAACACGTAAAAGTTTGTCAACTTCAGAAGTTTGGCCTAGAAACAAGAGAGAAA 257 AAGTTATAAAAGAACTCGTAAAAGTTTGTCAACTTCAG-AGTCTGG-C-AGAAACAAGAGAGAAA * * * * * * 403 CTATTCTCACCTAAAAAAGTTTATAATTCAGAGACCAAAAGTTGTTTACATAATGGCAATTATTT 319 CTATTCTCACCTAAAAAAGTTTATAATTCAAAAACCAAAAGTAGTTTACAGAATGACAATAATTT * * * * 468 ACACTAAATGATGCGATTTCTAGAGCATAGAATTTCTT 384 ACACTAAATAATGCGATTTCCAGAGCACAGAATTAC-T * 506 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCAAAATTAT-AAAGTAACTCG 1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAATGAA-CAAAATTATAAAAG-AACTCG *** * * 570 TAAAAGTTTT-TCAAGCTCGGAAGTTAGATCGAGAACCAA-AAGAGAAACAATTCTCAACTAAAT 64 -AAAA-TTTTGTCAAG-TTTAAAGTTAGGTCGAGAACCAAGAA-AGAAACAATTCTCACCTAAAT * * * * * * * 633 AAATTTTTCATT-AGAAGACTAGAAGTAGTTTA-AAAAATGACAACT-TTTAGACCTAATGATGT 125 AATTTTTTAATTCA-AAGACCAAAAGTTGTTTACAAAAA-GACAACTATTTAGACCAAATGATGA * * * * 695 GATTTTCCAAGCATGGACTGTACAGAAAATTACTCGAAGGAATCGATCTTCTTGAATACTTTAAT 188 GA-TTTCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAAT-GATCTTCTTGAATACTTTAAG * * * * 760 GAGCAAAAGTTATAAAAGTACTCGTAAAACTTTGTCAAGTTC-G-G-CT-G-AG-AACGAATAGA 251 GAGCAAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAACTTCAGAGTCTGGCAGAAAC-AAGAGA * * * * * * 819 GAAA-TAATTCTCACCTAAATAAGTTTTTAATTGAAAAACCGAAAGTAG-TTATAGAATGACAGT 315 GAAACT-ATTCTCACCTAAAAAAGTTTATAATTCAAAAACCAAAAGTAGTTTACAGAATGACAAT * * * * 882 AATTTAGACCT-AATAATGTGATTTCCCA-AGCACGGACTGTAC- 379 AATTTACA-CTAAATAATGCGATTT-CCAGAGCACAGAAT-TACT * 924 AATATATTG-TTGAAGGAATGGATCGTCTTGAATACTTTAATGAACAAAATTTATAAAAGAACAT 1 AA-A-ATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAATGAACAAAA-TTATAAAAGAAC-T * * ** * * 988 -GAAAATTTTGTCAAGTTTAAAGTTTGGCCGAGAACCAAGAAAGAAACAGCTATCACCTAAAGAA 62 CGAAAATTTTGTCAAGTTTAAAGTTAGGTCGAGAACCAAGAAAGAAACAATTCTCACCTAAATAA * * * 1052 TTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAAGACAACTATTTAAACAAAATGATGCGATT 127 TTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAAGACAACTATTTAGACCAAATGATGAGATT * * * * * 1117 TCCAAGCATGGAAAGTTCAAAAAATTGCTCGAAGGAATGGATCGTCTTAAATACTTTAAGGAGCC 192 TCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAAT-GATCTTCTTGAATACTTTAAGGAGCA * * * * 1182 AAAGTTATAAAAGAAATCGTAAAAGTTTGTCAACTTTGAAAGT-TCGGCCCAGAACCAAGAGAGA 256 AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAC-TTCAGAGTCT-GG--CAGAAACAAGAGAGA * * * * * * * * * * 1246 AATTATTCTTACCTAAATAAGTTTTTAATTCAAAGATCAAAAGTTGTTTACATAATAAC-ATCTA 317 AACTATTCTCACCTAAAAAAGTTTATAATTCAAAAACCAAAAGTAGTTTACAGAATGACAAT-AA * * ** ** * * 1310 TTTAGACCAAATGGTGCGATTTCTC-GAGCATGGAATGTTCC 381 TTTACACTAAATAATGCGATTTC-CAGAGCACAGAAT-TACT * * * 1351 AGAAATTGCTCGAAGGAATAGATCGTCTTGATTGCTTTAA 1 A-AAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAA Statistics Matches: 714, Mismatches: 126, Indels: 90 0.77 0.14 0.10 Matches are distributed among these distances: 417 156 0.22 418 41 0.06 419 81 0.11 420 63 0.09 422 1 0.00 423 1 0.00 424 1 0.00 425 51 0.07 426 49 0.07 427 159 0.22 428 110 0.15 429 1 0.00 ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29 Consensus pattern (420 bp): AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAATGAACAAAATTATAAAAGAACTCGAA AATTTTGTCAAGTTTAAAGTTAGGTCGAGAACCAAGAAAGAAACAATTCTCACCTAAATAATTTT TTAATTCAAAGACCAAAAGTTGTTTACAAAAAGACAACTATTTAGACCAAATGATGAGATTTCCA AGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGATCTTCTTGAATACTTTAAGGAGCAAAAGT TATAAAAGAACTCGTAAAAGTTTGTCAACTTCAGAGTCTGGCAGAAACAAGAGAGAAACTATTCT CACCTAAAAAAGTTTATAATTCAAAAACCAAAAGTAGTTTACAGAATGACAATAATTTACACTAA ATAATGCGATTTCCAGAGCACAGAATTACT Found at i:1238 original size:631 final size:635 Alignment explanation
Indices: 19--1390 Score: 1515 Period size: 631 Copynumber: 2.2 Consensus size: 635 9 AATAAAAGCT * * * 19 GTTTACAAAATGACAACTATTT-GACATAATGTTGTGATTTTCCAGGCATGGACTGTACAGAAAA 1 GTTTACAAAATGACAACTATTTAGACCTAATGATGTGATTTTCCAAGCATGGACTGTACAGAAAA * * 83 TTACTCGAAGGAATCGATCGTCTTGAATACGTTAATGAACAAAAGTTATAAAAGAACTCGTAAAT 66 TTACTCGAAGGAATCGATCGTCTTGAATACTTTAATGAACAAAAGTTATAAAAGAACTCGTAAAA * * * 148 GTTTGTCAAGTTTAAAGTTCGGTCGAGAACTAAGAAAGAAACAATTCTCACATAAATAATTTTTT 131 CTTTGTC------AAAGTTCGGTCGAGAACGAAGAAAGAAACAATTCTCACATAAATAAGTTTTT * * * ** 213 AATTCAAAGACCAAAAGTTGTTTACAAAACGATAACTAGTTAGACCAAATGATGAGATTCCCTGT 190 AATTCAAAAACCAAAAGTAGTTTACAAAACGATAACTA-TTAGACCAAATAATGAGATTCCCTAA ** * * * * ** 278 GCTTGGAATGTTCAGAAAATTGCTCGAAGGAATGGTTTGTCTTGATTACTGTAAGGAACTGAAGT 254 GCACGGAATGTACAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTGTAAGGAACAAAAGT * * * 343 TATAAAGAACACGTAAAAGTTTGTCAACTTCAGAAGTTTGGCCTAGAAACAAGAGAGAAACTATT 319 TATAAAGAACACGTAAAAGTTTGTCAACTTCAGAAGTTTGGCCGAGAAACAAGAAAGAAACTACT * * * * * * * * 408 CTCACCTAAAAAAGTTTATAATTCAGAGACCAAAAGTTGTTTACATAATGGCAATTATTTACACT 384 ATCACCTAAAAAAGTTTATAATTCAAAGACCAAAAGTTGTTTACAAAAAGACAACTATTTAAACA * * ** * 473 AAATGATGCGATTTCTAGAGCATAGAATTTCTTAAAATTGCTCGAAGGAATGGATCGTCTTGAAT 449 AAATGATGCGATTTCCAGAGCATAGAAGTTCAAAAAATTGCTCGAAGGAATGGATCGTCTTAAAT * * * * * * 538 ACTTTAAGGAATCAAAATTATAAAGTAACTCGTAAAAGTTTTTCAAGCTCGGAAGTTAGATCGAG 514 ACTTTAAGGAACCAAAATTATAAAGTAAATCGTAAAAGTTTGTCAAGCTCGAAAGTTAGACCCAG * * 603 AACCAAAAGAGAAACAATTCTCAACTAAATAAATTTTTCATT-AGAAGA-CTAGAAGTA 579 AACCAAAAGAGAAACAATTCTCAACTAAATAAATTTTTAATTCA-AAGATC-AAAAGTA * 660 GTTTAAAAAATGACAACT-TTTAGACCTAATGATGTGATTTTCCAAGCATGGACTGTACAGAAAA 1 GTTTACAAAATGACAACTATTTAGACCTAATGATGTGATTTTCCAAGCATGGACTGTACAGAAAA * * * 724 TTACTCGAAGGAATCGATCTTCTTGAATACTTTAATGAGCAAAAGTTATAAAAGTACTCGTAAAA 66 TTACTCGAAGGAATCGATCGTCTTGAATACTTTAATGAACAAAAGTTATAAAAGAACTCGTAAAA * * * * * 789 CTTTGTC-AAGTTCGG-CTGAGAACGAATAGAGAAATAATTCTCACCTAAATAAGTTTTTAATTG 131 CTTTGTCAAAGTTCGGTC-GAGAACGAAGAAAGAAACAATTCTCACATAAATAAGTTTTTAATTC * * * * * 852 AAAAACCGAAAGTAGTTATAGAATGAC-AGTAA-T-TTAGACCTAATAATGTGATTTCCC-AAGC 195 AAAAACCAAAAGTAGTT-TACAA-AACGA-TAACTATTAGACCAAATAATGAGA-TTCCCTAAGC * * * * * * 913 ACGGACTGTACA-ATATATTG-TTGAAGGAATGGATCGTCTTGAATACTTTAATGAACAAAATTT 256 ACGGAATGTACAGA-AAATTGCTCGAAGGAATGGATCGTCTTGAATACTGTAAGGAACAAAAGTT * * * * * 976 ATAAAAGAACATG-AAAATTTTGTCAAGTTTA-AAGTTTGGCCGAGAACCAAGAAAGAAAC-AGC 320 AT-AAAGAACACGTAAAAGTTTGTCAACTTCAGAAGTTTGGCCGAGAAACAAGAAAGAAACTA-C * * * 1038 TATCACCTAAAGAATTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAAGACAACTATTTAAAC 383 TATCACCTAAAAAAGTTTATAATTCAAAGACCAAAAGTTGTTTACAAAAAGACAACTATTTAAAC * 1103 AAAATGATGCGATTTCCA-AGCATGGAAAGTTCAAAAAATTGCTCGAAGGAATGGATCGTCTTAA 448 AAAATGATGCGATTTCCAGAGCATAG-AAGTTCAAAAAATTGCTCGAAGGAATGGATCGTCTTAA * * * * * 1167 ATACTTTAAGGAGCCAAAGTTATAAAAG-AAATCGTAAAAGTTTGTCAA-CTTTGAAAGTTCGGC 512 ATACTTTAAGGAACCAAAATTAT-AAAGTAAATCGTAAAAGTTTGTCAAGC-TCGAAAGTTAGAC * ** * * * * 1230 CCAGAACCAAGAGAGAAATTATTCTTACCTAAATAAGTTTTTAATTCAAAGATCAAAAGTT 575 CCAGAACCAAAAGAGAAACAATTCTCAACTAAATAAATTTTTAATTCAAAGATCAAAAGTA * * * * * * * * * 1291 GTTTACATAATAACATCTATTTAGACCAAATGGTGCGA-TTTCTCGAGCATGGAATGTTCCAG-A 1 GTTTACAAAATGACAACTATTTAGACCTAATGATGTGATTTTC-CAAGCATGGACTG-TACAGAA * * * * 1354 AATTGCTCGAAGGAATAGATCGTCTTGATTGCTTTAA 64 AATTACTCGAAGGAATCGATCGTCTTGAATACTTTAA Statistics Matches: 613, Mismatches: 101, Indels: 43 0.81 0.13 0.06 Matches are distributed among these distances: 630 8 0.01 631 241 0.39 632 118 0.19 633 44 0.07 634 66 0.11 635 6 0.01 636 5 0.01 640 3 0.00 641 122 0.20 ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29 Consensus pattern (635 bp): GTTTACAAAATGACAACTATTTAGACCTAATGATGTGATTTTCCAAGCATGGACTGTACAGAAAA TTACTCGAAGGAATCGATCGTCTTGAATACTTTAATGAACAAAAGTTATAAAAGAACTCGTAAAA CTTTGTCAAAGTTCGGTCGAGAACGAAGAAAGAAACAATTCTCACATAAATAAGTTTTTAATTCA AAAACCAAAAGTAGTTTACAAAACGATAACTATTAGACCAAATAATGAGATTCCCTAAGCACGGA ATGTACAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTGTAAGGAACAAAAGTTATAAAG AACACGTAAAAGTTTGTCAACTTCAGAAGTTTGGCCGAGAAACAAGAAAGAAACTACTATCACCT AAAAAAGTTTATAATTCAAAGACCAAAAGTTGTTTACAAAAAGACAACTATTTAAACAAAATGAT GCGATTTCCAGAGCATAGAAGTTCAAAAAATTGCTCGAAGGAATGGATCGTCTTAAATACTTTAA GGAACCAAAATTATAAAGTAAATCGTAAAAGTTTGTCAAGCTCGAAAGTTAGACCCAGAACCAAA AGAGAAACAATTCTCAACTAAATAAATTTTTAATTCAAAGATCAAAAGTA Done.